HEADER TRANSFERASE 24-JUN-13 4LDN TITLE CRYSTAL STRUCTURE OF A PUTATIVE PURINE NUCLEOSIDE PHOSPHORYLASE FROM TITLE 2 VIBRIO FISCHERI ES114 (TARGET NYSGRC-029521) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PURINE NUCLEOSIDE PHOSPHORYLASE DEOD-TYPE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PNP; COMPND 5 EC: 2.4.2.1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO FISCHERI; SOURCE 3 ORGANISM_TAXID: 312309; SOURCE 4 STRAIN: ES114; SOURCE 5 GENE: DEOD3, VF_A0968; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) CODONPLUS RIL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PSGC-HIS KEYWDS STRUCTURAL GENOMICS, NYSGRC, PSI-BIOLOGY, NEW YORK STRUCTURAL KEYWDS 2 GENOMICS RESEARCH CONSORTIUM, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR P.SAMPATHKUMAR,S.C.ALMO,NEW YORK STRUCTURAL GENOMICS RESEARCH AUTHOR 2 CONSORTIUM (NYSGRC) REVDAT 3 09-OCT-24 4LDN 1 REMARK SEQADV LINK REVDAT 2 15-NOV-17 4LDN 1 REMARK REVDAT 1 03-JUL-13 4LDN 0 JRNL AUTH P.SAMPATHKUMAR,M.AHMED,J.ATTONITO,R.BHOSLE,J.BONANNO, JRNL AUTH 2 S.CHAMALA,S.CHOWDHURY,G.EROMENOK,A.FISER,A.S.GLENN, JRNL AUTH 3 J.HAMMONDS,D.M.HIMMEL,B.HILLERICH,K.KHAFIZOV,J.LAFLEUR, JRNL AUTH 4 J.D.LOVE,M.STEAD,R.SEIDEL,R.TORO,L.L.MORISCO,S.S.SOJITRA, JRNL AUTH 5 S.R.WASSERMAN,J.SUAREZ,V.L.SCHRAMM,S.C.ALMO JRNL TITL CRYSTAL STRUCTURE OF A PUTATIVE PURINE NUCLEOSIDE JRNL TITL 2 PHOSPHORYLASE FROM VIBRIO FISCHERI ES114 (TARGET JRNL TITL 3 NYSGRC-029521) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.48 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0032 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.48 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.84 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 37970 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.164 REMARK 3 R VALUE (WORKING SET) : 0.162 REMARK 3 FREE R VALUE : 0.187 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1896 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.48 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.52 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2607 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.80 REMARK 3 BIN R VALUE (WORKING SET) : 0.2560 REMARK 3 BIN FREE R VALUE SET COUNT : 144 REMARK 3 BIN FREE R VALUE : 0.2430 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1901 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 30 REMARK 3 SOLVENT ATOMS : 164 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.39 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.62000 REMARK 3 B22 (A**2) : -0.62000 REMARK 3 B33 (A**2) : 2.01000 REMARK 3 B12 (A**2) : -0.62000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.069 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.069 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.052 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.410 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.972 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.964 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2037 ; 0.012 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1969 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2765 ; 1.636 ; 1.985 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4535 ; 0.768 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 266 ; 6.004 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 94 ;36.118 ;24.362 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 322 ;12.397 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;18.066 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 316 ; 0.087 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2310 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 464 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 999 ; 1.251 ; 1.574 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 998 ; 1.248 ; 1.570 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1253 ; 2.119 ; 2.354 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 4LDN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-JUN-13. REMARK 100 THE DEPOSITION ID IS D_1000080497. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-APR-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 10.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 31-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979310 REMARK 200 MONOCHROMATOR : DIAMOND(111) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX225HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37977 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.480 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 14.80 REMARK 200 R MERGE (I) : 0.11200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 23.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.48 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.51 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.8 REMARK 200 DATA REDUNDANCY IN SHELL : 13.50 REMARK 200 R MERGE FOR SHELL (I) : 0.80100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELX C, SHELXD REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.97 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.95 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN (20MM HEPES PH7.5, 150MM NACL, REMARK 280 5% GLYCEROL, AND 5MM DTT), RESERVOIR (MCSG2 #05 - 0.2 M LITHIUM REMARK 280 SULFATE, 0.1 M CAPS:NAOH PH 10.5, 1.2 M NAH2PO4/0.8 M K2HPO4), REMARK 280 CRYOPROTECTION (33% ETHYLENE GLYCOL), VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+2/3,-Z+2/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 81.55750 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 47.08724 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 15.11300 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 81.55750 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 47.08724 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 15.11300 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 81.55750 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 47.08724 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 15.11300 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 81.55750 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 47.08724 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 15.11300 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 81.55750 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 47.08724 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 15.11300 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 81.55750 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 47.08724 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 15.11300 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 94.17449 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 30.22600 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 94.17449 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 30.22600 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 94.17449 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 30.22600 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 94.17449 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 30.22600 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 94.17449 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 30.22600 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 94.17449 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 30.22600 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 300 REMARK: PROBABLE HEXAMER REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 28020 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 51840 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -82.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 4 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 45.33900 REMARK 350 BIOMT1 5 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 5 0.000000 0.000000 -1.000000 45.33900 REMARK 350 BIOMT1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 6 0.000000 0.000000 -1.000000 45.33900 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 C2 EDO A 306 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 432 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 457 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 477 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 533 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MSE A -21 REMARK 465 HIS A -20 REMARK 465 HIS A -19 REMARK 465 HIS A -18 REMARK 465 HIS A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 SER A -14 REMARK 465 SER A -13 REMARK 465 GLY A -12 REMARK 465 VAL A -11 REMARK 465 ASP A -10 REMARK 465 LEU A -9 REMARK 465 GLY A -8 REMARK 465 THR A -7 REMARK 465 GLU A -6 REMARK 465 GLU A 239 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OD2 ASP A 123 O HOH A 552 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 517 O HOH A 517 4556 2.10 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 25 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG A 25 NE - CZ - NH2 ANGL. DEV. = -4.2 DEGREES REMARK 500 ASP A 158 CB - CG - OD2 ANGL. DEV. = -6.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASP A 42 20.44 -152.96 REMARK 500 ARG A 44 19.68 56.73 REMARK 500 THR A 79 -86.25 -102.85 REMARK 500 LYS A 102 -4.91 82.09 REMARK 500 GLU A 180 -157.30 -150.94 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 307 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: NYSGRC-029521 RELATED DB: TARGETTRACK DBREF 4LDN A 1 239 UNP Q5DYV8 DEOD3_VIBF1 1 239 SEQADV 4LDN MSE A -21 UNP Q5DYV8 EXPRESSION TAG SEQADV 4LDN HIS A -20 UNP Q5DYV8 EXPRESSION TAG SEQADV 4LDN HIS A -19 UNP Q5DYV8 EXPRESSION TAG SEQADV 4LDN HIS A -18 UNP Q5DYV8 EXPRESSION TAG SEQADV 4LDN HIS A -17 UNP Q5DYV8 EXPRESSION TAG SEQADV 4LDN HIS A -16 UNP Q5DYV8 EXPRESSION TAG SEQADV 4LDN HIS A -15 UNP Q5DYV8 EXPRESSION TAG SEQADV 4LDN SER A -14 UNP Q5DYV8 EXPRESSION TAG SEQADV 4LDN SER A -13 UNP Q5DYV8 EXPRESSION TAG SEQADV 4LDN GLY A -12 UNP Q5DYV8 EXPRESSION TAG SEQADV 4LDN VAL A -11 UNP Q5DYV8 EXPRESSION TAG SEQADV 4LDN ASP A -10 UNP Q5DYV8 EXPRESSION TAG SEQADV 4LDN LEU A -9 UNP Q5DYV8 EXPRESSION TAG SEQADV 4LDN GLY A -8 UNP Q5DYV8 EXPRESSION TAG SEQADV 4LDN THR A -7 UNP Q5DYV8 EXPRESSION TAG SEQADV 4LDN GLU A -6 UNP Q5DYV8 EXPRESSION TAG SEQADV 4LDN ASN A -5 UNP Q5DYV8 EXPRESSION TAG SEQADV 4LDN LEU A -4 UNP Q5DYV8 EXPRESSION TAG SEQADV 4LDN TYR A -3 UNP Q5DYV8 EXPRESSION TAG SEQADV 4LDN PHE A -2 UNP Q5DYV8 EXPRESSION TAG SEQADV 4LDN GLN A -1 UNP Q5DYV8 EXPRESSION TAG SEQADV 4LDN SER A 0 UNP Q5DYV8 EXPRESSION TAG SEQRES 1 A 261 MSE HIS HIS HIS HIS HIS HIS SER SER GLY VAL ASP LEU SEQRES 2 A 261 GLY THR GLU ASN LEU TYR PHE GLN SER MSE SER THR PRO SEQRES 3 A 261 HIS ILE ASN ALA PRO LEU ASP ALA PHE ALA ASP THR ILE SEQRES 4 A 261 LEU MSE PRO GLY ASP PRO LEU ARG ALA LYS LEU ILE ALA SEQRES 5 A 261 GLU THR TYR LEU GLU ASN VAL VAL GLN VAL THR ASP VAL SEQRES 6 A 261 ARG GLY MSE LEU GLY PHE THR GLY GLU PHE LYS GLY ARG SEQRES 7 A 261 LYS ILE SER VAL MSE GLY HIS GLY MSE GLY ALA PRO SER SEQRES 8 A 261 ALA SER ILE TYR PHE HIS GLU LEU MSE THR THR TYR LYS SEQRES 9 A 261 VAL LYS ASN PHE ILE ARG ILE GLY SER CYS GLY ALA ILE SEQRES 10 A 261 HIS ASP ASP VAL LYS LEU LYS ASP LEU ILE VAL ALA ILE SEQRES 11 A 261 GLY ALA SER THR ASP SER LYS MSE ASN ARG ILE ARG PHE SEQRES 12 A 261 LYS ASP ASN ASP PHE ALA ALA THR ALA ASN TYR ASN MSE SEQRES 13 A 261 LEU SER GLU CYS VAL ASN THR LEU LYS THR THR ASP ILE SEQRES 14 A 261 ASN TYR LEU VAL GLY ASN VAL PHE SER SER ASP LEU PHE SEQRES 15 A 261 TYR ARG PRO ASP GLU GLU GLN TYR ASP MSE MSE ALA ARG SEQRES 16 A 261 TYR GLY ILE LEU GLY VAL GLU MSE GLU VAL ASN ALA LEU SEQRES 17 A 261 TYR SER ALA ALA ALA GLU ASN HIS CYS ASN ALA VAL ALA SEQRES 18 A 261 LEU CYS THR VAL THR ASP HIS ILE LYS ASN HIS GLU HIS SEQRES 19 A 261 LEU THR ALA ASP GLU ARG ARG THR GLU LEU HIS GLU MSE SEQRES 20 A 261 ILE ASN VAL ALA LEU ASP VAL ALA LEU LYS LEU PRO THR SEQRES 21 A 261 GLU MODRES 4LDN MSE A 1 MET SELENOMETHIONINE MODRES 4LDN MSE A 19 MET SELENOMETHIONINE MODRES 4LDN MSE A 46 MET SELENOMETHIONINE MODRES 4LDN MSE A 61 MET SELENOMETHIONINE MODRES 4LDN MSE A 65 MET SELENOMETHIONINE MODRES 4LDN MSE A 78 MET SELENOMETHIONINE MODRES 4LDN MSE A 116 MET SELENOMETHIONINE MODRES 4LDN MSE A 134 MET SELENOMETHIONINE MODRES 4LDN MSE A 170 MET SELENOMETHIONINE MODRES 4LDN MSE A 171 MET SELENOMETHIONINE MODRES 4LDN MSE A 181 MET SELENOMETHIONINE MODRES 4LDN MSE A 225 MET SELENOMETHIONINE HET MSE A 1 8 HET MSE A 19 8 HET MSE A 46 8 HET MSE A 61 8 HET MSE A 65 8 HET MSE A 78 8 HET MSE A 116 8 HET MSE A 134 13 HET MSE A 170 8 HET MSE A 171 8 HET MSE A 181 8 HET MSE A 225 8 HET PO4 A 301 5 HET PO4 A 302 5 HET EDO A 303 4 HET EDO A 304 4 HET EDO A 305 4 HET EDO A 306 4 HET EDO A 307 4 HETNAM MSE SELENOMETHIONINE HETNAM PO4 PHOSPHATE ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 1 MSE 12(C5 H11 N O2 SE) FORMUL 2 PO4 2(O4 P 3-) FORMUL 4 EDO 5(C2 H6 O2) FORMUL 9 HOH *164(H2 O) HELIX 1 1 ASN A -5 SER A 0 1 6 HELIX 2 2 ASP A 22 LEU A 34 1 13 HELIX 3 3 ASP A 42 MSE A 46 5 5 HELIX 4 4 GLY A 66 THR A 79 1 14 HELIX 5 5 LYS A 115 PHE A 121 1 7 HELIX 6 6 ASN A 131 THR A 144 1 14 HELIX 7 7 GLU A 165 TYR A 174 1 10 HELIX 8 8 GLU A 182 HIS A 194 1 13 HELIX 9 9 THR A 214 LEU A 236 1 23 SHEET 1 A10 GLU A 35 THR A 41 0 SHEET 2 A10 GLY A 48 PHE A 53 -1 O GLU A 52 N GLU A 35 SHEET 3 A10 ARG A 56 MSE A 61 -1 O ILE A 58 N GLY A 51 SHEET 4 A10 THR A 16 MSE A 19 1 N LEU A 18 O SER A 59 SHEET 5 A10 ASN A 85 ALA A 94 1 O ILE A 87 N MSE A 19 SHEET 6 A10 GLY A 178 GLU A 180 -1 O VAL A 179 N GLY A 93 SHEET 7 A10 TYR A 149 SER A 156 1 N PHE A 155 O GLU A 180 SHEET 8 A10 LEU A 104 THR A 112 1 N SER A 111 O SER A 156 SHEET 9 A10 ASN A 196 HIS A 206 -1 O CYS A 201 N ILE A 105 SHEET 10 A10 GLU A 211 HIS A 212 -1 O GLU A 211 N HIS A 206 SHEET 1 B 7 GLU A 35 THR A 41 0 SHEET 2 B 7 GLY A 48 PHE A 53 -1 O GLU A 52 N GLU A 35 SHEET 3 B 7 ARG A 56 MSE A 61 -1 O ILE A 58 N GLY A 51 SHEET 4 B 7 THR A 16 MSE A 19 1 N LEU A 18 O SER A 59 SHEET 5 B 7 ASN A 85 ALA A 94 1 O ILE A 87 N MSE A 19 SHEET 6 B 7 ASN A 196 HIS A 206 1 O LEU A 200 N GLY A 90 SHEET 7 B 7 GLU A 211 HIS A 212 -1 O GLU A 211 N HIS A 206 LINK C SER A 0 N MSE A 1 1555 1555 1.34 LINK C MSE A 1 N SER A 2 1555 1555 1.33 LINK C LEU A 18 N MSE A 19 1555 1555 1.33 LINK C MSE A 19 N PRO A 20 1555 1555 1.35 LINK C GLY A 45 N MSE A 46 1555 1555 1.33 LINK C MSE A 46 N LEU A 47 1555 1555 1.32 LINK C VAL A 60 N MSE A 61 1555 1555 1.33 LINK C MSE A 61 N GLY A 62 1555 1555 1.33 LINK C GLY A 64 N MSE A 65 1555 1555 1.31 LINK C MSE A 65 N GLY A 66 1555 1555 1.32 LINK C LEU A 77 N MSE A 78 1555 1555 1.33 LINK C MSE A 78 N THR A 79 1555 1555 1.32 LINK C LYS A 115 N MSE A 116 1555 1555 1.34 LINK C MSE A 116 N ASN A 117 1555 1555 1.32 LINK C ASN A 133 N MSE A 134 1555 1555 1.34 LINK C MSE A 134 N LEU A 135 1555 1555 1.32 LINK C ASP A 169 N MSE A 170 1555 1555 1.33 LINK C MSE A 170 N MSE A 171 1555 1555 1.33 LINK C MSE A 171 N ALA A 172 1555 1555 1.34 LINK C GLU A 180 N MSE A 181 1555 1555 1.34 LINK C MSE A 181 N GLU A 182 1555 1555 1.34 LINK C GLU A 224 N MSE A 225 1555 1555 1.34 LINK C MSE A 225 N ILE A 226 1555 1555 1.35 SITE 1 AC1 6 GLY A 21 ARG A 25 ARG A 44 ARG A 88 SITE 2 AC1 6 SER A 91 HOH A 404 SITE 1 AC2 4 HIS A 210 HIS A 212 HOH A 478 HOH A 537 SITE 1 AC3 5 ASN A 117 ARG A 120 PHE A 126 TYR A 174 SITE 2 AC3 5 SER A 188 SITE 1 AC4 3 TYR A 33 HIS A 223 HOH A 405 SITE 1 AC5 4 HIS A 96 ALA A 172 ILE A 176 HOH A 455 SITE 1 AC6 3 ARG A 44 MSE A 46 HOH A 482 SITE 1 AC7 4 THR A 145 ASN A 227 ASP A 231 HOH A 503 CRYST1 163.115 163.115 45.339 90.00 90.00 120.00 H 3 2 18 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.006131 0.003540 0.000000 0.00000 SCALE2 0.000000 0.007079 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022056 0.00000